Biochemistry Flashcards
Carbohydrates/ Lipids/ Protein Synthesis/ Nucleic Acid
Types of organic macromolecules in living organisms
- Carbohydrates (monomers)
- Lipids (polymers)
- Protein (monomers)
- Nucleic Acid (monomers)
Monomers
Small molecules
Polymers
Large molecules made of many monomers.
Dehydration Synthesis
Build a polymer by adding a monomer.
In the process, it releases a water molecule.
Hydrolysis
Break a polymer into a monomer.
Water molecule is added to new molecules.
Carbohydrate traits
- Energy storage
- Structural
- Signaling
- Hydrophilic
Monosaccharides
Are the monomers of all carbohydrates.
They’re composed of:
* 3 - 7 Carbons
* Same # of oxygen
* 2x as many Hydrogends
Typically form rings + taste sweet
ex: Glucose + Fructose
Disaccharides
2 monosaccharides as a molecule that often taste sweet.
ex: Sucrose = table sugar
2 glucose and 1 fructose
Polysaccharides
What are they + ones covered in class
Molecules of many monosaccharides.
* Starch - not made by humans, made by plants, a major form of E in the human diet
* Glucogen - made by humans, used to store E, in liver and tissue cells
* Other polysaccharides are used for structure and signaling
Lipid traits
- Lots of C + H
- Hydrophobic (Many hydrophobic chemicals that can turn into each other)
- Non-monomer
- Used for: E storage, Signaling, Insulation + cushioning
- Located in the Plasma membrane
Fatty Acids
are the simplest form of lipid.
If it has a long C-H chain = hydrophobic
If there’s a small carboxyl on top = hydrophilic
Saturated
fat
- No double bond
- Solid at room temp
- Less healthy - can clog vessels
- Comes from animals
Unsaturated
fats
- Some double bonds
- Liquid at room temp
- More healthy
- Comes from plants
Trans
fats
- Double bonds are going in the wrong direction
- Worse than saturated
- Comes from an artificial process
Triglycerides
- 1 glycerol (3 carbon sugar) + 3 fatty acids
- E storage in fat cells + liver
- Many types of cells in the body
Phosophilipids
MAJOR part of plasma membrane
* 2 Hydrophobic tails + hydrophilic head (contains P) making it Amphiphilic.
Amphiphilic
Molecule has hydrophobic + hydrophilic parts
Steroids
Lipid with 4 carbon rings.
Steroid hormones
Chemicals that signal whole body
Protein traits
- Do stuff
- Generate movement
- Control chemical reactions (enzymes)
- Structural
- Move things across membranes
- Signaling + receptors (detect other chemical signals)
- Composed of long chain amino acids connected by peptide bonds.
Amino Acids
Definition + traits
Are the monomers of proteins.
1. Amino group NH3+ (hydrophilic)
2. Carboxyl group CO2- (hydrophilic)
3. Central C (hydrophilic) attached to other 4 parts
4. Side chain
* 20 types of AA w/ a different side chain giving it different chemical properties which affects how the AA works.
Peptide bonds
attach 2 amino acids together.
* Amino group of one connected to carboxyl group of another
* example of Dehydration synthesis
Protein sequence
Definition + function
is the order of amino acids in protein.
* Sequence of AAs determines the chemical property of protein + function of protein
* Folds into a 3D shape - shape is critical for function
* Shape of protein matches the shape of molecules it interacts with
Denature
process in which protein becomes unwound, loses its shape. Can occur when the wrong pH and/or high heat is present.
Protein synthesis
Occurs through a 2 part process
1. Transcription - RNA synthesis 2 (RNA acts as an intermediary)
2. Translation - DNA codes for how and when to make proteins (Proteins do everything in the cell)
Transcription
is the process of turning DNA to RNA (word for word).
1. Small part of DNA molecule is copied to RNA
2. RNA nucleotides brought in to match the ones on DNA
– Happens in the nucleus by proteins (enzymes)
Transcription vs DNA Replication
Transcription is like DNA replication:
* DNA strands separated
* Nucleotides brought in to match with DNA
Ways transcription is different:
* RNA nucleotides present
* Only one strand is copied
* Small part of DNA is copied
* RNA comes off at the end and the DNA comes back together
DNA Replication Steps
- DNA nucleotides added
- Both strands copied
- Whole strand is copied
- 2 new DNA strands made with 1 old and 1 new strand
Translation
is protein synthesis (mRNA sequence → protein sequence) that occurs in the cytoplasm by ribosomes.
* Sequence of nucleotides in mRNA corresponds to sequence of AA in protein
* mRNA is read to make protein in correct sequence
* 3 types of RNA involved
mRNA
messengerRNA is a sequence of nucleotides that matches up with the sequence of amino acids in protein
Codon
are a group of 3 nucleotides in mRNA that codes for one amino acid.
* 64 possible codons - many code for the same amino acid
Genetic code
What does it do?
shows which codons code which amino acids, codes all 20 amino acids.
tRNA
transferRNA brings amino acids to the ribosomes to assemble into proteins, making it the physical embodiment of genetic code.
* One side has 3 nucleotides that match with 3 nucleotides of a codon
* The other side has amino acids for the codon
* Each codon has a different tRNA
Ribosomes
Definition
are composed of protein and rRNA (ribosomal RNA) and are located in the cytoplasm.
Ribosomes role in protein synthesis
- Reads along mRNA
- Brings in tRNA to match up with codons on mRNA
- Connects AA from tRNA into protein - this makes a peptide bond
- After adding each new AA to protein
Ribosome moves down mRNA to next codon - Brings tRNA that matches next codon
- Binds AA from tRNA to the growing protein
- Repeats until it reaches stop codon
Post-translational modification
further changes proteins after translation and gives them their 3D shape.
Nucleic Acids
= DNA + RNA
DNA
- Giant polymers with 100s of nucleotides
- Information transfer between parent and child
- 2 strands of nucleotides attached one after another
- Formatted as phosphate - sugar - phosphate
- Stores info on how + when to make proteins
RNA
Definition + functions
is composed of shorter strands, the nucleotides are slightly different, and is a single strand that helps a cell read DNA + make protein.
Functions:
* Information storage
* Energy storage
* Signaling
Nucleotides
Definition + traits
are the monomers of nucleic acids.
Composed of:
1. Central sugar (ribose or deoxyribose)
2. 1 - 3 Phosphate groups (PO4-)
3. Base: (A) - T / (G) - C / (T) - A / (C) - G
ATP
Definition + traits
= adenosine triphosphate, a nucleotide with 3 phosphates.
* Used throughout cell for energy
* Used by proteins
* Used to do many things
Enzymes
Definition + purposes
are proteins that stimulate chemical reactions.
* Each enzyme stimulates a different chemical reaction
* Enzymes lower activation energy, thus speeding up a chemical reaction and doesn’t effect chemical equilibrium - just reaches it faster
* The cell can control what chemical reactions are happening by controlling what enzymes are present
* Can also stimulate endergonic reactions
Active side
Definition + Process
part of an enzyme that blinds substrates, matches shape + chemical composition.
1. Binds substrate at active side
2. Stimulates chemical reaction
3. Releases the products
Exergonic reaction
spontaneous chemical reactions
Activation Energy
Energy you have to put in to start a chemical reaction (even 4 exergonic), slowing down the chemical reaction.
Endergonic reactions
Endergonic reactions need energy
Energy from exergonic reactions can be used to stimulate the endergonic.
ATP Coupling
Occurs when energy is released from ATP to be used in another chemical reaction.
Links an exergonic reaction to an endergonic reaction.
Gene
Part of the DNA molecule that codes for mRNA.
Expressing a gene
is to transcribe and translate the gene and make protein that it codes from.
* Different cell types express different genes
Control regions
are part of the DNA that doesn’t code for protein - is close to the genes that do.
Transcription factors
Definition + factors
are proteins that bind to the control regions of DNA. Binding turns on and off the expression of nearby genes.
* Which proteins you are making depends on which transcription factors are in cell
* One transition factor can control the expression of many genes, determining what protein a cell makes and determines function of cell
Chemical signals
reffers to when one cell releases a chemical signal and another cell detects then responds.
Ligand
Definition + traits
a chemical signal that the cell responds to. Different ligands have different effects.
* Can be bound to the membrane of the cell so 2 cells have to touch for the 2nd cell to detect
* Can be proteins, single amino acids, steroids, polysaccharides bound to the cells membrane, lipids
* Some can be released - traveling short distances and signal nearly cells, some travel long distances
Hormones
= endocrines
* chemical signals released into the blood and signals cells thought the body
Ligand receptor
responds to different ligands, if a cell doesn’t have a receptor then it wont respond.
Epinephrine
How it works in the body
- blood vessels near skeletal muscles dilate
- visceral blood vessels constrict
* different vessels have different receptors for epinephrine
Receptor proteins
Definition + traits
transmembrane proteins that binds to ligand.
* Induces a response in the cells
* Different receptors bing to different ligands
* Different receptors have different effects
Agonists
Are another chemical that binds on a receptor and it has same effect as a ligand.
Antagonists
are another chemical that binds to the receptor but has no effect. This stops ligand from binding receptors so it doesn’t work.
Single transduction
Definition + process
How a signal from outside the cell leads to a response inside the cell.
1. Receptor bings ligand + changes shape
2. Receptor activates 2nd messengers
3. Responses are generated by 2nd messengers inside the cell
2nd messengers
Signals inside the cell that are activated by a receptor when it binds to a ligand.
* Can activate more 2nd messengers.
Signalling Cascade
One 2nd messenger activates another creating a cascading effect. At each stage one 2nd Messenger can activate many 2nd messengers at next step.
* 1 activated receptor can have millions of activated 2nd messengers.
Membrane Potential
The electrical charge across the membrane can act as a 2nd messenger.
The membrane potential changes when ion channels open and close. This can activate proteins.
Ca++ signalling /
Intracellular Ca++
Occurs when lots of Ca++ in extra cellular fluid + SER (smooth endoplasmic reticulum) → opens Ca++ channel → Ca++ flows in → proteins bind to the Ca++ → become activated
Can act as a 2nd messenger
Phosphorylation
Phosphate group is added to a protein top activate or deactivate the protein.
- Kinases are enzymes that add phosphates to proteins
- Phosphatases are enzymes that remove phosphates from proteins
Responses generated by 2nd messengers in the cell
List them
- Turn on and off motor protein or an enzyme
- Change gene expression
- Change membrane proteins
Intracellular Receptors
Receptors inside the cell that:
1. can only detect ligands that can go through the phospholipid bilayer (gasses + steroids)
2. act slower than extracellular receptors
3. often directly affect gene expression
Extracellular Receptors
Transmembrane proteins that detect and respond to chemicals outside the cell.
Direct: proteins, amino acids, carbs + some lipids
Respond: quickly but move transient
G-Protein Coupled Receptors (GPCR)
The most common receptors bound to the cytoplasmic side of the membrane. Also considered a peripheral membrane protein because it’s bound to the inside of a membrane.
Different ones respond to different ligands, when bound it activates the receptor.
Other effects on the cell: actuates enzymes, opens ion channels
Ligand Gated Ion Channel
An ion channel that opens or closes when it binds a ligand, changing the membrane potential of the cell
